Targeted Proteomics Data
AMP PD features two separate Targeted Proteomics datasets. AMP PD Release 3.0 contains data generated from a total of 3050 samples from 413 participants. The data, provided by two data providers, was generated using Olink Explore 1536 methodology. Release 3.0 data contains a total of 1641 Plasma samples and 1409 CSF samples. Each participant sample run contains at least three longitudinal timepoints. The two separate targeted proteomics data sets are: D01 and D02. Dataset D01 was provided to AMP PD in 2021 and contains 743 CSF and 743 matched Plasma samples from 212 participants. Dataset D02 was provided to AMP PD in 2022 and contains 666 CSF samples and 898 Plasma samples from 240 participants. Together, these make up the 3050 samples from 413 unique participants.
These Targeted Proteomics datasets contains eight unfiltered NPX files from four separate Panels for both Plasma and CSF samples. The four targeted proteomics panels are Cardiometabolic, Inflammation, Neurology, and Oncology. Within the data release, all datasets are listed under the main datasets tab within the proteomics folder and are split into four separate datasets. The data is split by tissue source (CSF, Plasma) and data set number (D01, D02). From there, the main folders for each data set contain data from all four panels in both long and matrix format. An additional format is provided in the olink-explore-format folder. This format is provided for those who wish to use Olink specific tools. Each dataset also contains a samples metadata sheet for user reference.
Data has been reformatted from the original format to contain AMP PD specific participant and sample IDs. Additional QC columns have been added to the data in order to provide additional information for flagged or passed samples. The released data has accompanying Terra notebooks, ranging from “Getting Started” notebooks which help users get familiar with the data and eventually assign case and control to samples, to QC notebooks to show users QC criteria used in flagging samples and analysis notebooks to perform simple data visualizations.
As AMP PD accumulates datasets of the same source tissue and compatible methods, normalized aggregate datasets will appear in the releases directory. Datasets in the datasets directory should not be combined in researchers' analyses without first assessing compatibility and normalizing their values.
What's on this page:
Baseline | 3M | 6M | 9M | 12M | 18M | 24M | 30M | 36M | 42M | 48M | 54M | 60M | 72M | 84M | 96M | Total | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PDBP | Plasma | 111 | 0 | 2 | 0 | 91 | 28 | 114 | 0 | 110 | 0 | 48 | 0 | 17 | 0 | 0 | 0 | 521 |
CSF | 111 | 0 | 2 | 0 | 91 | 28 | 114 | 0 | 110 | 0 | 48 | 0 | 17 | 0 | 0 | 0 | 521 | |
PPMI | Plasma | 263 | 26 | 125 | 9 | 128 | 24 | 166 | 26 | 94 | 18 | 148 | 15 | 55 | 7 | 5 | 1 | 1120 |
CSF | 244 | 5 | 111 | 0 | 109 | 0 | 152 | 1 | 84 | 0 | 133 | 1 | 43 | 0 | 5 | 1 | 888 |
Sample Selection Criteria
The criteria used to select these samples were as follows:
- Samples for three timepoint or more available
- Participant samples selected were from participants who had previously generated corresponding Whole Genome Sequencing or Transcriptomic data on the AMP PD Knowledge Platform
- All CSF samples selected had hemoglobin < 100 ng/mL to assure limited blood contamination
- All Plasma and CSF samples were collected under similar protocols
AMP PD Quality control of the preview release data was performed by Victoria Dardov from Technome as part of a contract with the Foundation for the National Institutes of Health (FNIH).
Information here was prepared by the Olink Proteomics in consultation with the AMP PD Proteomics Working Group.
Method
Proximity Extension Assay for Targeted Proteomics
Normalized Protein Expression (NPX) quantifies the relative amount of a specific protein. This is determined by performing an immunoassay for a targeted protein. Antibodies that bind to a protein of interest contain unique sequences that are extended, amplified and subsequently detected and quantified by NGS. The amount of this sequence is normalized to standard plate controls to give relative quantities of targeted proteins.
Assay Controls Summary
Extensive quality control is performed for each assay in order to control and assess technical performance of the assay at each step. This ensures generation of reliable data.
AMP PD Controls
AMP-PD quality control further examines the data and includes sample, run and control sample QC.
Generating NPX values
The Explore system´s raw data output are NGS counts, where each combination of an assay and sample is given an integer value based on the number of DNA copies detected. These raw data counts are converted into NPX values for use in downstream statistical analysis.